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Crystal structure of ebinur lake virus cap snatching endonuclease in complex with inhibitor 16
Analyse Crystal structure of ebinur lake virus cap snatching endonuclease in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EX7
- Type
- protein
- Length
- 701 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase
- EC
- 2.7.7.48
- UniProt
- A0A059WLS9
- Ligands
- 1I6, MN, CL
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Replicase (EC 2.7.7.48) | protein | 172 | 52% helix, 14% strand | A0A059WLS9 |
| C | Replicase (EC 2.7.7.48) | protein | 177 | 50% helix, 14% strand | A0A059WLS9 |
| D | Replicase (EC 2.7.7.48) | protein | 180 | 53% helix, 13% strand | A0A059WLS9 |
Ligands and binding sites
- 1I6 · Methyl (Z)-4-(4-(4-chlorobenzyl)-1-(3-methoxybenzyl) piperidin-4-yl)-2-hydroxy-4-oxobut-2-enoate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.58 | 0.75 | 41 | empty |
| 2 | 132 | 0.54 | 0.81 | 26 | empty |
| 3 | 172 | 0.44 | 0.74 | 23 | empty |
| 4 | 60 | 0.32 | 0.76 | 12 | empty |
| 5 | 54 | 0.29 | 0.75 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 530 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 327 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 270 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 85 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 56 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7EX7 · Crystal structure of Ebinur Lake virus cap snatching endonuclease in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A059WLS9
- Elsewhere: RCSB PDB 7EX7 · PDBe 7EX7 · UniProt A0A059WLS9
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